rs11048230

Variant names:

• chr12-25772238-T-C
• rs11048230
• ENST00000773355.1:n.103-8042A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773355.1(ENSG00000256440):​n.103-8042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,070 control chromosomes in the GnomAD database, including 2,903 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2903 hom., cov: 31)
• Consequence: ENSG00000256440 ENST00000773355.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862
• Publications: 3 publications found

Genes affected

ENSG00000256440 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256440	ENST00000773355.1	n.103-8042A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24672 AN: 151952 Hom.: 2898 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24714 AN: 152070 Hom.: 2903 Cov.: 31 AF XY: 0.161 AC XY: 11970 AN XY: 74354

African (AFR) AF: 0.335 AC: 13866 AN: 41422

American (AMR) AF: 0.0976 AC: 1490 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.0210 AC: 109 AN: 5188

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10594

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.0950 AC: 6461 AN: 67986

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.140 Hom.: 373

Bravo AF: 0.168

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11048230; hg19: chr12-25925172;